9QT6 | pdb_00009qt6

Crystal structure of HPK1 T165E/S171E in complex with pyrazine carboxamide inhibitor


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.76 Å
  • R-Value Free: 
    0.226 (Depositor), 0.218 (DCC) 
  • R-Value Work: 
    0.196 (Depositor), 0.187 (DCC) 
  • R-Value Observed: 
    0.198 (Depositor) 

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

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Ligand Structure Quality Assessment 


This is version 1.4 of the entry. See complete history

Literature

Synthetic chemistry enabling the discovery and development of a series of pyrazoles as HPK1 inhibitors.

Metrano, A.J.Morrill, L.A.Bommakanti, G.Casella, R.Cook, S.Escobar, R.A.Giblin, K.A.Gosselin, E.Grebe, T.Hariparsad, N.Howells, R.Lamont, G.M.Mele, D.A.Pflug, A.Proia, T.A.Rezaei, H.Richter, M.Richards, R.San Martin, M.Schimpl, M.Schuller, A.G.Sha, L.Sheppeck 2nd, J.E.Song, K.Tang, H.Wagner, D.J.Wang, J.Wu, A.Wu, D.Wu, Y.Xu, K.Ye, M.Shields, J.D.Grimster, N.P.

(2025) RSC Med Chem 16: 3522-3529

  • DOI: https://doi.org/10.1039/d5md00309a
  • Primary Citation Related Structures: 
    9QT6

  • PubMed Abstract: 

    Hematopoietic progenitor kinase 1 (HPK1) is a negative regulator of T-cell signaling. Inhibition of HPK1 with small molecules has been shown to reinvigorate the immune system toward fighting tumours in preclinical models, thus it holds promise as a therapeutic strategy in cancer immunotherapy. Herein we report a series of pyrazine carboxamide pyrazoles as selective inhibitors of HPK1. Key to our approach was the development of late-stage functionalisation chemistry which allowed for rapid SAR generation. Through these efforts, we discovered difluoroethyl pyrazole 16a, an in vivo tool which elicited the desired pharmacodynamic response in mice. Further, we describe the optimization of synthetic chemistry which could support preclinical studies of a member of this series of substituted pyrazoles.


  • Organizational Affiliation
    • Oncology R&D, AstraZeneca Waltham MA 02451 USA anthony.metrano@astrazeneca.com lucas.morrill@astrazeneca.com.

Macromolecule Content 

  • Total Structure Weight: 33.4 kDa 
  • Atom Count: 2,406 
  • Modeled Residue Count: 285 
  • Deposited Residue Count: 294 
  • Unique protein chains: 1

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
Mitogen-activated protein kinase kinase kinase kinase 1294Homo sapiensMutation(s): 2 
Gene Names: MAP4K1HPK1
EC: 2.7.11.1
UniProt & NIH Common Fund Data Resources
Find proteins for Q92918 (Homo sapiens)
Explore Q92918 
Go to UniProtKB:  Q92918
PHAROS:  Q92918
GTEx:  ENSG00000104814 
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ92918
Sequence Annotations
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Reference Sequence

Small Molecules

Ligands 2 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
A1JAF
(Subject of Investigation/LOI)

Query on A1JAF



Download:Ideal Coordinates CCD File
B [auth A]3-[(1,3-dimethylpyrazol-4-yl)amino]-5-(methylamino)-6-(3-methylimidazo[4,5-c]pyridin-7-yl)pyrazine-2-carboxamide
C18 H20 N10 O
BUGHKAJGIGJJGX-UHFFFAOYSA-N
EDO

Query on EDO



Download:Ideal Coordinates CCD File
C [auth A]1,2-ETHANEDIOL
C2 H6 O2
LYCAIKOWRPUZTN-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.76 Å
  • R-Value Free:  0.226 (Depositor), 0.218 (DCC) 
  • R-Value Work:  0.196 (Depositor), 0.187 (DCC) 
  • R-Value Observed: 0.198 (Depositor) 
Space Group: C 1 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 76.19α = 90
b = 68.1β = 96.33
c = 58.43γ = 90
Software Package:
Software NamePurpose
MOSFLMdata reduction
Aimlessdata scaling
STARANISOdata scaling
BUSTERrefinement
XDSdata reduction
AMoREphasing

Structure Validation

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Ligand Structure Quality Assessment 


Entry History 

& Funding Information

Deposition Data

  • Released Date: 2025-05-28 
  • Deposition Author(s): Schimpl, M.

Funding OrganizationLocationGrant Number
Not funded--

Revision History  (Full details and data files)

  • Version 1.0: 2025-05-28
    Type: Initial release
  • Version 1.1: 2025-07-02
    Changes: Database references
  • Version 1.2: 2025-07-09
    Changes: Database references
  • Version 1.3: 2025-07-23
    Changes: Database references
  • Version 1.4: 2025-09-03
    Changes: Database references